## Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
##   object 'config' not found

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Normalization: Viral read count

Canonic TSS dynamics

Those reads were counted only, where the 5-prime adapters were “correct” (according to LoRTIA)

Statistics of counts

Difference from mean

Varcoeff

Clustering of samples

## Bootstrap (r = 0.49)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.7)... Done.
## Bootstrap (r = 0.8)... Done.
## Bootstrap (r = 0.9)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.29)... Done.
## Bootstrap (r = 1.39)... Done.

The sample 48h_3 stands out!

Filtering of samples

Clustering of genes into de-novo clusters using hierarchial clustering

Cluster memberships

## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.58)... Done.
## Bootstrap (r = 0.69)... Done.
## Bootstrap (r = 0.77)... Done.
## Bootstrap (r = 0.88)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.08)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.27)... Done.
## Bootstrap (r = 1.38)... Done.

Optimal number of clusters

Find the optimal number of clusters to cut the tree at and calculate

Clustering statistics: Cluster number: 5

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  2:       1    ORF4 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  3:       1    ORF5 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  4:       1    ORF7 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  5:       1    ORF9 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  6:       1   ORF10 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  7:       1   ORF17 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  8:       1   ORF20 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  9:       1   ORF21 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 10:       1   ORF30 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 11:       1   ORF31 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 12:       1   ORF34 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 13:       1   ORF38 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 14:       1   ORF50 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 15:       1   ORF53 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 16:       1   ORF56 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 17:       1   ORF61 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 18:       1   ORF63 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 19:       1  NOIR_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 20:       1 ORF65_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 21:       1 ORF67_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 22:       1   ORF69 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 23:       1  NOIR_2 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 24:       2    ORF2 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 25:       2    ORF3 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 26:       2    ORF8 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 27:       2   ORF11 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 28:       2   ORF14 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 29:       2   ORF18 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 30:       2   ORF19 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 31:       2   ORF22 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 32:       2   ORF23 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 33:       2   ORF24 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 34:       2   ORF25 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 35:       2   ORF26 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 36:       2   ORF27 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 37:       2   ORF28 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 38:       2   ORF29 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 39:       2   ORF32 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 40:       2   ORF33 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 41:       2 ORF35.5 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 42:       2   ORF36 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 43:       2   ORF37 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 44:       2   ORF39 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 45:       2     CTO 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 46:       2   ORF40 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 47:       2   ORF42 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 48:       2   ORF43 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 49:       2   ORF44 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 50:       2   ORF46 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 51:       2   ORF49 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 52:       2   ORF51 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 53:       2   ORF55 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 54:       2   ORF58 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 55:       2   ORF59 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 56:       2   ORF62 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 57:       2 ORF66_1 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 58:       2   ORF68 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 59:       2   ORF73 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 60:       2   ORF74 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 61:       2   ORF76 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 62:       3    ORF6 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 63:       3   ORF70 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 64:       4   ORF12 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 65:       4   ORF13 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 66:       4   ORF15 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 67:       4   ORF16 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 68:       4   ORF35 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 69:       4   ORF41 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 70:       4   ORF45 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 71:       4   ORF48 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 72:       4   ORF52 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 73:       4   ORF54 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 74:       4   ORF57 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 75:       4   ORF60 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 76:       4   ORF71 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 77:       4   ORF72 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 78:       5 ORF64_1 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 79:       5   ORF75 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.004376930 -1.8294074 0.9239714 0.05335458
##  2: 0.004376930 -1.8294074 0.9239714 0.05335458
##  3: 0.004376930 -1.8294074 0.9239714 0.05335458
##  4: 0.004376930 -1.8294074 0.9239714 0.05335458
##  5: 0.004376930 -1.8294074 0.9239714 0.05335458
##  6: 0.004376930 -1.8294074 0.9239714 0.05335458
##  7: 0.004376930 -1.8294074 0.9239714 0.05335458
##  8: 0.004376930 -1.8294074 0.9239714 0.05335458
##  9: 0.004376930 -1.8294074 0.9239714 0.05335458
## 10: 0.004376930 -1.8294074 0.9239714 0.05335458
## 11: 0.004376930 -1.8294074 0.9239714 0.05335458
## 12: 0.004376930 -1.8294074 0.9239714 0.05335458
## 13: 0.004376930 -1.8294074 0.9239714 0.05335458
## 14: 0.004376930 -1.8294074 0.9239714 0.05335458
## 15: 0.004376930 -1.8294074 0.9239714 0.05335458
## 16: 0.004376930 -1.8294074 0.9239714 0.05335458
## 17: 0.004376930 -1.8294074 0.9239714 0.05335458
## 18: 0.004376930 -1.8294074 0.9239714 0.05335458
## 19: 0.004376930 -1.8294074 0.9239714 0.05335458
## 20: 0.004376930 -1.8294074 0.9239714 0.05335458
## 21: 0.004376930 -1.8294074 0.9239714 0.05335458
## 22: 0.004376930 -1.8294074 0.9239714 0.05335458
## 23: 0.004376930 -1.8294074 0.9239714 0.05335458
## 24: 0.005023951 -1.1447013 0.6730592 0.16333723
## 25: 0.005023951 -1.1447013 0.6730592 0.16333723
## 26: 0.005023951 -1.1447013 0.6730592 0.16333723
## 27: 0.005023951 -1.1447013 0.6730592 0.16333723
## 28: 0.005023951 -1.1447013 0.6730592 0.16333723
## 29: 0.005023951 -1.1447013 0.6730592 0.16333723
## 30: 0.005023951 -1.1447013 0.6730592 0.16333723
## 31: 0.005023951 -1.1447013 0.6730592 0.16333723
## 32: 0.005023951 -1.1447013 0.6730592 0.16333723
## 33: 0.005023951 -1.1447013 0.6730592 0.16333723
## 34: 0.005023951 -1.1447013 0.6730592 0.16333723
## 35: 0.005023951 -1.1447013 0.6730592 0.16333723
## 36: 0.005023951 -1.1447013 0.6730592 0.16333723
## 37: 0.005023951 -1.1447013 0.6730592 0.16333723
## 38: 0.005023951 -1.1447013 0.6730592 0.16333723
## 39: 0.005023951 -1.1447013 0.6730592 0.16333723
## 40: 0.005023951 -1.1447013 0.6730592 0.16333723
## 41: 0.005023951 -1.1447013 0.6730592 0.16333723
## 42: 0.005023951 -1.1447013 0.6730592 0.16333723
## 43: 0.005023951 -1.1447013 0.6730592 0.16333723
## 44: 0.005023951 -1.1447013 0.6730592 0.16333723
## 45: 0.005023951 -1.1447013 0.6730592 0.16333723
## 46: 0.005023951 -1.1447013 0.6730592 0.16333723
## 47: 0.005023951 -1.1447013 0.6730592 0.16333723
## 48: 0.005023951 -1.1447013 0.6730592 0.16333723
## 49: 0.005023951 -1.1447013 0.6730592 0.16333723
## 50: 0.005023951 -1.1447013 0.6730592 0.16333723
## 51: 0.005023951 -1.1447013 0.6730592 0.16333723
## 52: 0.005023951 -1.1447013 0.6730592 0.16333723
## 53: 0.005023951 -1.1447013 0.6730592 0.16333723
## 54: 0.005023951 -1.1447013 0.6730592 0.16333723
## 55: 0.005023951 -1.1447013 0.6730592 0.16333723
## 56: 0.005023951 -1.1447013 0.6730592 0.16333723
## 57: 0.005023951 -1.1447013 0.6730592 0.16333723
## 58: 0.005023951 -1.1447013 0.6730592 0.16333723
## 59: 0.005023951 -1.1447013 0.6730592 0.16333723
## 60: 0.005023951 -1.1447013 0.6730592 0.16333723
## 61: 0.005023951 -1.1447013 0.6730592 0.16333723
## 62: 0.004866876 -1.7084109 1.0563865 0.51628007
## 63: 0.004866876 -1.7084109 1.0563865 0.51628007
## 64: 0.004845179 -1.7779128 1.0925743 0.04880686
## 65: 0.004845179 -1.7779128 1.0925743 0.04880686
## 66: 0.004845179 -1.7779128 1.0925743 0.04880686
## 67: 0.004845179 -1.7779128 1.0925743 0.04880686
## 68: 0.004845179 -1.7779128 1.0925743 0.04880686
## 69: 0.004845179 -1.7779128 1.0925743 0.04880686
## 70: 0.004845179 -1.7779128 1.0925743 0.04880686
## 71: 0.004845179 -1.7779128 1.0925743 0.04880686
## 72: 0.004845179 -1.7779128 1.0925743 0.04880686
## 73: 0.004845179 -1.7779128 1.0925743 0.04880686
## 74: 0.004845179 -1.7779128 1.0925743 0.04880686
## 75: 0.004845179 -1.7779128 1.0925743 0.04880686
## 76: 0.004845179 -1.7779128 1.0925743 0.04880686
## 77: 0.004845179 -1.7779128 1.0925743 0.04880686
## 78: 0.004635436 -0.5796832 1.2128574 0.32603176
## 79: 0.004635436 -0.5796832 1.2128574 0.32603176
##           se.bp          v         c       pchi

## [1] "ORF67_1" "ORF32"   "ORF58"   "ORF33"   "ORF35.5" "ORF25"   "ORF27"  
## [8] "ORF62"
## [1] 8
## character(0)
## [1] 0

Clustering statistics: Cluster number: 6

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  2:       1    ORF4 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  3:       1    ORF5 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  4:       1    ORF7 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  5:       1    ORF9 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  6:       1   ORF10 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  7:       1   ORF17 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  8:       1   ORF20 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  9:       1   ORF21 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 10:       1   ORF30 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 11:       1   ORF31 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 12:       1   ORF34 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 13:       1   ORF38 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 14:       1   ORF50 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 15:       1   ORF53 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 16:       1   ORF56 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 17:       1   ORF61 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 18:       1   ORF63 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 19:       1  NOIR_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 20:       1 ORF65_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 21:       1 ORF67_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 22:       1   ORF69 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 23:       1  NOIR_2 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 24:       2    ORF2 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 25:       2    ORF3 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 26:       2   ORF11 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 27:       2   ORF14 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 28:       2   ORF18 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 29:       2   ORF19 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 30:       2   ORF26 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 31:       2   ORF28 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 32:       2   ORF29 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 33:       2   ORF37 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 34:       2   ORF51 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 35:       2   ORF55 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 36:       2 ORF66_1 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 37:       2   ORF73 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 38:       2   ORF76 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 39:       3    ORF6 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 40:       3   ORF70 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 41:       4    ORF8 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 42:       4   ORF22 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 43:       4   ORF23 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 44:       4   ORF24 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 45:       4   ORF25 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 46:       4   ORF27 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 47:       4   ORF32 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 48:       4   ORF33 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 49:       4 ORF35.5 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 50:       4   ORF36 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 51:       4   ORF39 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 52:       4     CTO 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 53:       4   ORF40 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 54:       4   ORF42 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 55:       4   ORF43 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 56:       4   ORF44 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 57:       4   ORF46 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 58:       4   ORF49 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 59:       4   ORF58 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 60:       4   ORF59 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 61:       4   ORF62 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 62:       4   ORF68 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 63:       4   ORF74 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 64:       5   ORF12 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 65:       5   ORF13 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 66:       5   ORF15 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 67:       5   ORF16 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 68:       5   ORF35 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 69:       5   ORF41 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 70:       5   ORF45 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 71:       5   ORF48 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 72:       5   ORF52 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 73:       5   ORF54 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 74:       5   ORF57 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 75:       5   ORF60 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 76:       5   ORF71 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 77:       5   ORF72 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 78:       6 ORF64_1 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 79:       6   ORF75 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.004376930 -1.8294074 0.9239714 0.05335458
##  2: 0.004376930 -1.8294074 0.9239714 0.05335458
##  3: 0.004376930 -1.8294074 0.9239714 0.05335458
##  4: 0.004376930 -1.8294074 0.9239714 0.05335458
##  5: 0.004376930 -1.8294074 0.9239714 0.05335458
##  6: 0.004376930 -1.8294074 0.9239714 0.05335458
##  7: 0.004376930 -1.8294074 0.9239714 0.05335458
##  8: 0.004376930 -1.8294074 0.9239714 0.05335458
##  9: 0.004376930 -1.8294074 0.9239714 0.05335458
## 10: 0.004376930 -1.8294074 0.9239714 0.05335458
## 11: 0.004376930 -1.8294074 0.9239714 0.05335458
## 12: 0.004376930 -1.8294074 0.9239714 0.05335458
## 13: 0.004376930 -1.8294074 0.9239714 0.05335458
## 14: 0.004376930 -1.8294074 0.9239714 0.05335458
## 15: 0.004376930 -1.8294074 0.9239714 0.05335458
## 16: 0.004376930 -1.8294074 0.9239714 0.05335458
## 17: 0.004376930 -1.8294074 0.9239714 0.05335458
## 18: 0.004376930 -1.8294074 0.9239714 0.05335458
## 19: 0.004376930 -1.8294074 0.9239714 0.05335458
## 20: 0.004376930 -1.8294074 0.9239714 0.05335458
## 21: 0.004376930 -1.8294074 0.9239714 0.05335458
## 22: 0.004376930 -1.8294074 0.9239714 0.05335458
## 23: 0.004376930 -1.8294074 0.9239714 0.05335458
## 24: 0.005023951 -1.1447013 0.6730592 0.16333723
## 25: 0.005023951 -1.1447013 0.6730592 0.16333723
## 26: 0.005023951 -1.1447013 0.6730592 0.16333723
## 27: 0.005023951 -1.1447013 0.6730592 0.16333723
## 28: 0.005023951 -1.1447013 0.6730592 0.16333723
## 29: 0.005023951 -1.1447013 0.6730592 0.16333723
## 30: 0.005023951 -1.1447013 0.6730592 0.16333723
## 31: 0.005023951 -1.1447013 0.6730592 0.16333723
## 32: 0.005023951 -1.1447013 0.6730592 0.16333723
## 33: 0.005023951 -1.1447013 0.6730592 0.16333723
## 34: 0.005023951 -1.1447013 0.6730592 0.16333723
## 35: 0.005023951 -1.1447013 0.6730592 0.16333723
## 36: 0.005023951 -1.1447013 0.6730592 0.16333723
## 37: 0.005023951 -1.1447013 0.6730592 0.16333723
## 38: 0.005023951 -1.1447013 0.6730592 0.16333723
## 39: 0.004866876 -1.7084109 1.0563865 0.51628007
## 40: 0.004866876 -1.7084109 1.0563865 0.51628007
## 41: 0.004845179 -1.7779128 1.0925743 0.04880686
## 42: 0.004845179 -1.7779128 1.0925743 0.04880686
## 43: 0.004845179 -1.7779128 1.0925743 0.04880686
## 44: 0.004845179 -1.7779128 1.0925743 0.04880686
## 45: 0.004845179 -1.7779128 1.0925743 0.04880686
## 46: 0.004845179 -1.7779128 1.0925743 0.04880686
## 47: 0.004845179 -1.7779128 1.0925743 0.04880686
## 48: 0.004845179 -1.7779128 1.0925743 0.04880686
## 49: 0.004845179 -1.7779128 1.0925743 0.04880686
## 50: 0.004845179 -1.7779128 1.0925743 0.04880686
## 51: 0.004845179 -1.7779128 1.0925743 0.04880686
## 52: 0.004845179 -1.7779128 1.0925743 0.04880686
## 53: 0.004845179 -1.7779128 1.0925743 0.04880686
## 54: 0.004845179 -1.7779128 1.0925743 0.04880686
## 55: 0.004845179 -1.7779128 1.0925743 0.04880686
## 56: 0.004845179 -1.7779128 1.0925743 0.04880686
## 57: 0.004845179 -1.7779128 1.0925743 0.04880686
## 58: 0.004845179 -1.7779128 1.0925743 0.04880686
## 59: 0.004845179 -1.7779128 1.0925743 0.04880686
## 60: 0.004845179 -1.7779128 1.0925743 0.04880686
## 61: 0.004845179 -1.7779128 1.0925743 0.04880686
## 62: 0.004845179 -1.7779128 1.0925743 0.04880686
## 63: 0.004845179 -1.7779128 1.0925743 0.04880686
## 64: 0.004635436 -0.5796832 1.2128574 0.32603176
## 65: 0.004635436 -0.5796832 1.2128574 0.32603176
## 66: 0.004635436 -0.5796832 1.2128574 0.32603176
## 67: 0.004635436 -0.5796832 1.2128574 0.32603176
## 68: 0.004635436 -0.5796832 1.2128574 0.32603176
## 69: 0.004635436 -0.5796832 1.2128574 0.32603176
## 70: 0.004635436 -0.5796832 1.2128574 0.32603176
## 71: 0.004635436 -0.5796832 1.2128574 0.32603176
## 72: 0.004635436 -0.5796832 1.2128574 0.32603176
## 73: 0.004635436 -0.5796832 1.2128574 0.32603176
## 74: 0.004635436 -0.5796832 1.2128574 0.32603176
## 75: 0.004635436 -0.5796832 1.2128574 0.32603176
## 76: 0.004635436 -0.5796832 1.2128574 0.32603176
## 77: 0.004635436 -0.5796832 1.2128574 0.32603176
## 78: 0.005225222 -1.2149856 0.9031625 0.82402823
## 79: 0.005225222 -1.2149856 0.9031625 0.82402823
##           se.bp          v         c       pchi

## [1] "ORF67_1" "ORF9"    "ORF73"   "ORF32"   "ORF62"   "ORF45"
## [1] 6
## character(0)
## [1] 0

Clustering statistics: Cluster number: 7

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  2:       1    ORF4 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  3:       1    ORF5 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  4:       1    ORF7 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  5:       1    ORF9 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  6:       1   ORF10 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  7:       1   ORF17 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  8:       1   ORF20 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  9:       1   ORF21 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 10:       1   ORF30 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 11:       1   ORF31 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 12:       1   ORF34 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 13:       1   ORF38 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 14:       1   ORF50 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 15:       1   ORF53 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 16:       1   ORF56 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 17:       1   ORF61 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 18:       1   ORF63 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 19:       1  NOIR_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 20:       1 ORF65_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 21:       1 ORF67_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 22:       1   ORF69 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 23:       1  NOIR_2 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 24:       2    ORF2 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 25:       2    ORF3 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 26:       2   ORF11 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 27:       2   ORF14 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 28:       2   ORF18 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 29:       2   ORF19 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 30:       2   ORF26 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 31:       2   ORF28 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 32:       2   ORF29 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 33:       2   ORF37 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 34:       2   ORF51 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 35:       2   ORF55 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 36:       2 ORF66_1 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 37:       2   ORF73 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 38:       2   ORF76 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 39:       3    ORF6 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 40:       3   ORF70 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 41:       4    ORF8 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 42:       4   ORF22 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 43:       4   ORF23 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 44:       4   ORF24 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 45:       4   ORF25 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 46:       4   ORF27 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 47:       4   ORF32 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 48:       4   ORF33 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 49:       4 ORF35.5 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 50:       4   ORF36 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 51:       4   ORF39 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 52:       4     CTO 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 53:       4   ORF40 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 54:       4   ORF42 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 55:       4   ORF43 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 56:       4   ORF44 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 57:       4   ORF46 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 58:       4   ORF49 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 59:       4   ORF58 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 60:       4   ORF59 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 61:       4   ORF62 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 62:       4   ORF68 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 63:       4   ORF74 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 64:       5   ORF12 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 65:       5   ORF13 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 66:       5   ORF15 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 67:       5   ORF16 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 68:       5   ORF35 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 69:       5   ORF41 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 70:       5   ORF48 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 71:       5   ORF52 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 72:       5   ORF54 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 73:       5   ORF57 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 74:       5   ORF60 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 75:       5   ORF71 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 76:       5   ORF72 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 77:       6   ORF45 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 78:       7 ORF64_1 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 79:       7   ORF75 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.004376930 -1.8294074 0.9239714 0.05335458
##  2: 0.004376930 -1.8294074 0.9239714 0.05335458
##  3: 0.004376930 -1.8294074 0.9239714 0.05335458
##  4: 0.004376930 -1.8294074 0.9239714 0.05335458
##  5: 0.004376930 -1.8294074 0.9239714 0.05335458
##  6: 0.004376930 -1.8294074 0.9239714 0.05335458
##  7: 0.004376930 -1.8294074 0.9239714 0.05335458
##  8: 0.004376930 -1.8294074 0.9239714 0.05335458
##  9: 0.004376930 -1.8294074 0.9239714 0.05335458
## 10: 0.004376930 -1.8294074 0.9239714 0.05335458
## 11: 0.004376930 -1.8294074 0.9239714 0.05335458
## 12: 0.004376930 -1.8294074 0.9239714 0.05335458
## 13: 0.004376930 -1.8294074 0.9239714 0.05335458
## 14: 0.004376930 -1.8294074 0.9239714 0.05335458
## 15: 0.004376930 -1.8294074 0.9239714 0.05335458
## 16: 0.004376930 -1.8294074 0.9239714 0.05335458
## 17: 0.004376930 -1.8294074 0.9239714 0.05335458
## 18: 0.004376930 -1.8294074 0.9239714 0.05335458
## 19: 0.004376930 -1.8294074 0.9239714 0.05335458
## 20: 0.004376930 -1.8294074 0.9239714 0.05335458
## 21: 0.004376930 -1.8294074 0.9239714 0.05335458
## 22: 0.004376930 -1.8294074 0.9239714 0.05335458
## 23: 0.004376930 -1.8294074 0.9239714 0.05335458
## 24: 0.005023951 -1.1447013 0.6730592 0.16333723
## 25: 0.005023951 -1.1447013 0.6730592 0.16333723
## 26: 0.005023951 -1.1447013 0.6730592 0.16333723
## 27: 0.005023951 -1.1447013 0.6730592 0.16333723
## 28: 0.005023951 -1.1447013 0.6730592 0.16333723
## 29: 0.005023951 -1.1447013 0.6730592 0.16333723
## 30: 0.005023951 -1.1447013 0.6730592 0.16333723
## 31: 0.005023951 -1.1447013 0.6730592 0.16333723
## 32: 0.005023951 -1.1447013 0.6730592 0.16333723
## 33: 0.005023951 -1.1447013 0.6730592 0.16333723
## 34: 0.005023951 -1.1447013 0.6730592 0.16333723
## 35: 0.005023951 -1.1447013 0.6730592 0.16333723
## 36: 0.005023951 -1.1447013 0.6730592 0.16333723
## 37: 0.005023951 -1.1447013 0.6730592 0.16333723
## 38: 0.005023951 -1.1447013 0.6730592 0.16333723
## 39: 0.004866876 -1.7084109 1.0563865 0.51628007
## 40: 0.004866876 -1.7084109 1.0563865 0.51628007
## 41: 0.004845179 -1.7779128 1.0925743 0.04880686
## 42: 0.004845179 -1.7779128 1.0925743 0.04880686
## 43: 0.004845179 -1.7779128 1.0925743 0.04880686
## 44: 0.004845179 -1.7779128 1.0925743 0.04880686
## 45: 0.004845179 -1.7779128 1.0925743 0.04880686
## 46: 0.004845179 -1.7779128 1.0925743 0.04880686
## 47: 0.004845179 -1.7779128 1.0925743 0.04880686
## 48: 0.004845179 -1.7779128 1.0925743 0.04880686
## 49: 0.004845179 -1.7779128 1.0925743 0.04880686
## 50: 0.004845179 -1.7779128 1.0925743 0.04880686
## 51: 0.004845179 -1.7779128 1.0925743 0.04880686
## 52: 0.004845179 -1.7779128 1.0925743 0.04880686
## 53: 0.004845179 -1.7779128 1.0925743 0.04880686
## 54: 0.004845179 -1.7779128 1.0925743 0.04880686
## 55: 0.004845179 -1.7779128 1.0925743 0.04880686
## 56: 0.004845179 -1.7779128 1.0925743 0.04880686
## 57: 0.004845179 -1.7779128 1.0925743 0.04880686
## 58: 0.004845179 -1.7779128 1.0925743 0.04880686
## 59: 0.004845179 -1.7779128 1.0925743 0.04880686
## 60: 0.004845179 -1.7779128 1.0925743 0.04880686
## 61: 0.004845179 -1.7779128 1.0925743 0.04880686
## 62: 0.004845179 -1.7779128 1.0925743 0.04880686
## 63: 0.004845179 -1.7779128 1.0925743 0.04880686
## 64: 0.004635436 -0.5796832 1.2128574 0.32603176
## 65: 0.004635436 -0.5796832 1.2128574 0.32603176
## 66: 0.004635436 -0.5796832 1.2128574 0.32603176
## 67: 0.004635436 -0.5796832 1.2128574 0.32603176
## 68: 0.004635436 -0.5796832 1.2128574 0.32603176
## 69: 0.004635436 -0.5796832 1.2128574 0.32603176
## 70: 0.004635436 -0.5796832 1.2128574 0.32603176
## 71: 0.004635436 -0.5796832 1.2128574 0.32603176
## 72: 0.004635436 -0.5796832 1.2128574 0.32603176
## 73: 0.004635436 -0.5796832 1.2128574 0.32603176
## 74: 0.004635436 -0.5796832 1.2128574 0.32603176
## 75: 0.004635436 -0.5796832 1.2128574 0.32603176
## 76: 0.004635436 -0.5796832 1.2128574 0.32603176
## 77: 0.005225222 -1.2149856 0.9031625 0.82402823
## 78: 0.004968046 -1.4394451 0.8949157 0.71371866
## 79: 0.004968046 -1.4394451 0.8949157 0.71371866
##           se.bp          v         c       pchi

## [1] "ORF67_1" "ORF9"    "ORF73"   "ORF27"   "ORF32"   "ORF62"
## [1] 6
## character(0)
## [1] 0

Clustering statistics: Cluster number: 10

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  2:       1    ORF5 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  3:       1   ORF10 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  4:       1   ORF17 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  5:       1   ORF30 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  6:       1   ORF53 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  7:       1   ORF63 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  8:       1 ORF65_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  9:       1 ORF67_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 10:       1   ORF69 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 11:       1  NOIR_2 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 12:       2    ORF2 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 13:       2    ORF3 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 14:       2   ORF11 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 15:       2   ORF14 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 16:       2   ORF18 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 17:       2   ORF19 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 18:       2   ORF26 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 19:       2   ORF29 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 20:       2   ORF37 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 21:       2   ORF51 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 22:       2   ORF55 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 23:       2 ORF66_1 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 24:       2   ORF73 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 25:       2   ORF76 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 26:       3    ORF4 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 27:       3    ORF7 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 28:       3    ORF9 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 29:       3   ORF20 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 30:       3   ORF21 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 31:       3   ORF31 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 32:       3   ORF34 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 33:       3   ORF38 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 34:       3   ORF50 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 35:       3   ORF56 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 36:       3   ORF61 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 37:       3  NOIR_1 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 38:       4    ORF6 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 39:       4   ORF70 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 40:       5    ORF8 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 41:       5   ORF22 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 42:       5   ORF23 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 43:       5   ORF24 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 44:       5   ORF25 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 45:       5   ORF33 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 46:       5 ORF35.5 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 47:       5   ORF36 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 48:       5   ORF39 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 49:       5     CTO 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 50:       5   ORF40 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 51:       5   ORF42 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 52:       5   ORF43 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 53:       5   ORF44 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 54:       5   ORF46 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 55:       5   ORF49 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 56:       5   ORF58 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 57:       5   ORF62 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 58:       5   ORF68 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 59:       5   ORF74 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 60:       6   ORF12 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 61:       6   ORF13 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 62:       6   ORF15 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 63:       6   ORF16 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 64:       6   ORF35 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 65:       6   ORF41 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 66:       6   ORF48 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 67:       6   ORF52 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 68:       6   ORF54 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 69:       6   ORF57 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 70:       6   ORF60 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 71:       6   ORF71 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 72:       6   ORF72 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 73:       7   ORF27 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 74:       7   ORF32 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 75:       7   ORF59 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 76:       8   ORF28 0.7904904 0.9662526 0.4397080 0.025548629 0.0060702951
## 77:       9   ORF45 0.5315416 0.9101709 0.3441776 0.044014262 0.0134541621
## 78:      10 ORF64_1 0.9770332 0.9982955 0.5151696 0.004496626 0.0004626117
## 79:      10   ORF75 0.9770332 0.9982955 0.5151696 0.004496626 0.0004626117
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.004376930 -1.8294074 0.9239714 0.05335458
##  2: 0.004376930 -1.8294074 0.9239714 0.05335458
##  3: 0.004376930 -1.8294074 0.9239714 0.05335458
##  4: 0.004376930 -1.8294074 0.9239714 0.05335458
##  5: 0.004376930 -1.8294074 0.9239714 0.05335458
##  6: 0.004376930 -1.8294074 0.9239714 0.05335458
##  7: 0.004376930 -1.8294074 0.9239714 0.05335458
##  8: 0.004376930 -1.8294074 0.9239714 0.05335458
##  9: 0.004376930 -1.8294074 0.9239714 0.05335458
## 10: 0.004376930 -1.8294074 0.9239714 0.05335458
## 11: 0.004376930 -1.8294074 0.9239714 0.05335458
## 12: 0.005023951 -1.1447013 0.6730592 0.16333723
## 13: 0.005023951 -1.1447013 0.6730592 0.16333723
## 14: 0.005023951 -1.1447013 0.6730592 0.16333723
## 15: 0.005023951 -1.1447013 0.6730592 0.16333723
## 16: 0.005023951 -1.1447013 0.6730592 0.16333723
## 17: 0.005023951 -1.1447013 0.6730592 0.16333723
## 18: 0.005023951 -1.1447013 0.6730592 0.16333723
## 19: 0.005023951 -1.1447013 0.6730592 0.16333723
## 20: 0.005023951 -1.1447013 0.6730592 0.16333723
## 21: 0.005023951 -1.1447013 0.6730592 0.16333723
## 22: 0.005023951 -1.1447013 0.6730592 0.16333723
## 23: 0.005023951 -1.1447013 0.6730592 0.16333723
## 24: 0.005023951 -1.1447013 0.6730592 0.16333723
## 25: 0.005023951 -1.1447013 0.6730592 0.16333723
## 26: 0.004866876 -1.7084109 1.0563865 0.51628007
## 27: 0.004866876 -1.7084109 1.0563865 0.51628007
## 28: 0.004866876 -1.7084109 1.0563865 0.51628007
## 29: 0.004866876 -1.7084109 1.0563865 0.51628007
## 30: 0.004866876 -1.7084109 1.0563865 0.51628007
## 31: 0.004866876 -1.7084109 1.0563865 0.51628007
## 32: 0.004866876 -1.7084109 1.0563865 0.51628007
## 33: 0.004866876 -1.7084109 1.0563865 0.51628007
## 34: 0.004866876 -1.7084109 1.0563865 0.51628007
## 35: 0.004866876 -1.7084109 1.0563865 0.51628007
## 36: 0.004866876 -1.7084109 1.0563865 0.51628007
## 37: 0.004866876 -1.7084109 1.0563865 0.51628007
## 38: 0.004845179 -1.7779128 1.0925743 0.04880686
## 39: 0.004845179 -1.7779128 1.0925743 0.04880686
## 40: 0.004635436 -0.5796832 1.2128574 0.32603176
## 41: 0.004635436 -0.5796832 1.2128574 0.32603176
## 42: 0.004635436 -0.5796832 1.2128574 0.32603176
## 43: 0.004635436 -0.5796832 1.2128574 0.32603176
## 44: 0.004635436 -0.5796832 1.2128574 0.32603176
## 45: 0.004635436 -0.5796832 1.2128574 0.32603176
## 46: 0.004635436 -0.5796832 1.2128574 0.32603176
## 47: 0.004635436 -0.5796832 1.2128574 0.32603176
## 48: 0.004635436 -0.5796832 1.2128574 0.32603176
## 49: 0.004635436 -0.5796832 1.2128574 0.32603176
## 50: 0.004635436 -0.5796832 1.2128574 0.32603176
## 51: 0.004635436 -0.5796832 1.2128574 0.32603176
## 52: 0.004635436 -0.5796832 1.2128574 0.32603176
## 53: 0.004635436 -0.5796832 1.2128574 0.32603176
## 54: 0.004635436 -0.5796832 1.2128574 0.32603176
## 55: 0.004635436 -0.5796832 1.2128574 0.32603176
## 56: 0.004635436 -0.5796832 1.2128574 0.32603176
## 57: 0.004635436 -0.5796832 1.2128574 0.32603176
## 58: 0.004635436 -0.5796832 1.2128574 0.32603176
## 59: 0.004635436 -0.5796832 1.2128574 0.32603176
## 60: 0.005225222 -1.2149856 0.9031625 0.82402823
## 61: 0.005225222 -1.2149856 0.9031625 0.82402823
## 62: 0.005225222 -1.2149856 0.9031625 0.82402823
## 63: 0.005225222 -1.2149856 0.9031625 0.82402823
## 64: 0.005225222 -1.2149856 0.9031625 0.82402823
## 65: 0.005225222 -1.2149856 0.9031625 0.82402823
## 66: 0.005225222 -1.2149856 0.9031625 0.82402823
## 67: 0.005225222 -1.2149856 0.9031625 0.82402823
## 68: 0.005225222 -1.2149856 0.9031625 0.82402823
## 69: 0.005225222 -1.2149856 0.9031625 0.82402823
## 70: 0.005225222 -1.2149856 0.9031625 0.82402823
## 71: 0.005225222 -1.2149856 0.9031625 0.82402823
## 72: 0.005225222 -1.2149856 0.9031625 0.82402823
## 73: 0.004968046 -1.4394451 0.8949157 0.71371866
## 74: 0.004968046 -1.4394451 0.8949157 0.71371866
## 75: 0.004968046 -1.4394451 0.8949157 0.71371866
## 76: 0.005268284 -0.8383279 0.9900376 0.17121312
## 77: 0.005000790 -0.4703599 0.8714482 0.43210675
## 78: 0.005399375 -1.4831325 1.4450987 0.32741114
## 79: 0.005399375 -1.4831325 1.4450987 0.32741114
##           se.bp          v         c       pchi

## [1] "ORF55" "ORF73" "ORF62" "ORF27" "ORF32" "ORF59"
## [1] 6
## [1] "ORF45"
## [1] 1

Clustering statistics: Cluster number: 12

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  2:       1    ORF5 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  3:       1   ORF10 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  4:       1   ORF17 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  5:       1   ORF30 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  6:       1   ORF53 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  7:       1   ORF63 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  8:       1 ORF65_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  9:       1 ORF67_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 10:       1   ORF69 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 11:       1  NOIR_2 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 12:       2    ORF2 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 13:       2    ORF3 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 14:       2   ORF11 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 15:       2   ORF14 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 16:       2   ORF18 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 17:       2   ORF19 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 18:       2   ORF26 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 19:       2   ORF29 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 20:       2   ORF37 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 21:       2   ORF51 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 22:       2   ORF55 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 23:       2 ORF66_1 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 24:       2   ORF73 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 25:       2   ORF76 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 26:       3    ORF4 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 27:       3    ORF9 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 28:       3   ORF20 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 29:       3   ORF21 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 30:       3   ORF31 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 31:       3   ORF34 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 32:       3   ORF38 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 33:       3   ORF50 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 34:       3   ORF61 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 35:       4    ORF6 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 36:       4   ORF70 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 37:       5    ORF7 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 38:       5   ORF56 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 39:       5  NOIR_1 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 40:       6    ORF8 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 41:       6   ORF22 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 42:       6   ORF23 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 43:       6   ORF24 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 44:       6   ORF25 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 45:       6   ORF33 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 46:       6 ORF35.5 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 47:       6   ORF36 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 48:       6   ORF39 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 49:       6     CTO 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 50:       6   ORF40 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 51:       6   ORF42 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 52:       6   ORF43 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 53:       6   ORF44 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 54:       6   ORF46 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 55:       6   ORF49 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 56:       6   ORF58 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 57:       6   ORF62 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 58:       6   ORF68 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 59:       6   ORF74 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 60:       7   ORF12 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 61:       7   ORF13 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 62:       7   ORF15 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 63:       7   ORF16 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 64:       7   ORF35 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 65:       7   ORF41 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 66:       7   ORF48 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 67:       7   ORF52 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 68:       7   ORF54 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 69:       7   ORF57 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 70:       7   ORF60 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 71:       7   ORF71 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 72:       7   ORF72 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 73:       8   ORF27 0.7904904 0.9662526 0.4397080 0.025548629 0.0060702951
## 74:       8   ORF59 0.7904904 0.9662526 0.4397080 0.025548629 0.0060702951
## 75:       9   ORF28 0.5315416 0.9101709 0.3441776 0.044014262 0.0134541621
## 76:      10   ORF32 0.9770332 0.9982955 0.5151696 0.004496626 0.0004626117
## 77:      11   ORF45 0.6926659 0.9668711 0.2610828 0.038775743 0.0066333119
## 78:      12 ORF64_1 0.5500885 0.9292526 0.2941077 0.045701573 0.0115867217
## 79:      12   ORF75 0.5500885 0.9292526 0.2941077 0.045701573 0.0115867217
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.004376930 -1.8294074 0.9239714 0.05335458
##  2: 0.004376930 -1.8294074 0.9239714 0.05335458
##  3: 0.004376930 -1.8294074 0.9239714 0.05335458
##  4: 0.004376930 -1.8294074 0.9239714 0.05335458
##  5: 0.004376930 -1.8294074 0.9239714 0.05335458
##  6: 0.004376930 -1.8294074 0.9239714 0.05335458
##  7: 0.004376930 -1.8294074 0.9239714 0.05335458
##  8: 0.004376930 -1.8294074 0.9239714 0.05335458
##  9: 0.004376930 -1.8294074 0.9239714 0.05335458
## 10: 0.004376930 -1.8294074 0.9239714 0.05335458
## 11: 0.004376930 -1.8294074 0.9239714 0.05335458
## 12: 0.005023951 -1.1447013 0.6730592 0.16333723
## 13: 0.005023951 -1.1447013 0.6730592 0.16333723
## 14: 0.005023951 -1.1447013 0.6730592 0.16333723
## 15: 0.005023951 -1.1447013 0.6730592 0.16333723
## 16: 0.005023951 -1.1447013 0.6730592 0.16333723
## 17: 0.005023951 -1.1447013 0.6730592 0.16333723
## 18: 0.005023951 -1.1447013 0.6730592 0.16333723
## 19: 0.005023951 -1.1447013 0.6730592 0.16333723
## 20: 0.005023951 -1.1447013 0.6730592 0.16333723
## 21: 0.005023951 -1.1447013 0.6730592 0.16333723
## 22: 0.005023951 -1.1447013 0.6730592 0.16333723
## 23: 0.005023951 -1.1447013 0.6730592 0.16333723
## 24: 0.005023951 -1.1447013 0.6730592 0.16333723
## 25: 0.005023951 -1.1447013 0.6730592 0.16333723
## 26: 0.004866876 -1.7084109 1.0563865 0.51628007
## 27: 0.004866876 -1.7084109 1.0563865 0.51628007
## 28: 0.004866876 -1.7084109 1.0563865 0.51628007
## 29: 0.004866876 -1.7084109 1.0563865 0.51628007
## 30: 0.004866876 -1.7084109 1.0563865 0.51628007
## 31: 0.004866876 -1.7084109 1.0563865 0.51628007
## 32: 0.004866876 -1.7084109 1.0563865 0.51628007
## 33: 0.004866876 -1.7084109 1.0563865 0.51628007
## 34: 0.004866876 -1.7084109 1.0563865 0.51628007
## 35: 0.004845179 -1.7779128 1.0925743 0.04880686
## 36: 0.004845179 -1.7779128 1.0925743 0.04880686
## 37: 0.004635436 -0.5796832 1.2128574 0.32603176
## 38: 0.004635436 -0.5796832 1.2128574 0.32603176
## 39: 0.004635436 -0.5796832 1.2128574 0.32603176
## 40: 0.005225222 -1.2149856 0.9031625 0.82402823
## 41: 0.005225222 -1.2149856 0.9031625 0.82402823
## 42: 0.005225222 -1.2149856 0.9031625 0.82402823
## 43: 0.005225222 -1.2149856 0.9031625 0.82402823
## 44: 0.005225222 -1.2149856 0.9031625 0.82402823
## 45: 0.005225222 -1.2149856 0.9031625 0.82402823
## 46: 0.005225222 -1.2149856 0.9031625 0.82402823
## 47: 0.005225222 -1.2149856 0.9031625 0.82402823
## 48: 0.005225222 -1.2149856 0.9031625 0.82402823
## 49: 0.005225222 -1.2149856 0.9031625 0.82402823
## 50: 0.005225222 -1.2149856 0.9031625 0.82402823
## 51: 0.005225222 -1.2149856 0.9031625 0.82402823
## 52: 0.005225222 -1.2149856 0.9031625 0.82402823
## 53: 0.005225222 -1.2149856 0.9031625 0.82402823
## 54: 0.005225222 -1.2149856 0.9031625 0.82402823
## 55: 0.005225222 -1.2149856 0.9031625 0.82402823
## 56: 0.005225222 -1.2149856 0.9031625 0.82402823
## 57: 0.005225222 -1.2149856 0.9031625 0.82402823
## 58: 0.005225222 -1.2149856 0.9031625 0.82402823
## 59: 0.005225222 -1.2149856 0.9031625 0.82402823
## 60: 0.004968046 -1.4394451 0.8949157 0.71371866
## 61: 0.004968046 -1.4394451 0.8949157 0.71371866
## 62: 0.004968046 -1.4394451 0.8949157 0.71371866
## 63: 0.004968046 -1.4394451 0.8949157 0.71371866
## 64: 0.004968046 -1.4394451 0.8949157 0.71371866
## 65: 0.004968046 -1.4394451 0.8949157 0.71371866
## 66: 0.004968046 -1.4394451 0.8949157 0.71371866
## 67: 0.004968046 -1.4394451 0.8949157 0.71371866
## 68: 0.004968046 -1.4394451 0.8949157 0.71371866
## 69: 0.004968046 -1.4394451 0.8949157 0.71371866
## 70: 0.004968046 -1.4394451 0.8949157 0.71371866
## 71: 0.004968046 -1.4394451 0.8949157 0.71371866
## 72: 0.004968046 -1.4394451 0.8949157 0.71371866
## 73: 0.005268284 -0.8383279 0.9900376 0.17121312
## 74: 0.005268284 -0.8383279 0.9900376 0.17121312
## 75: 0.005000790 -0.4703599 0.8714482 0.43210675
## 76: 0.005399375 -1.4831325 1.4450987 0.32741114
## 77: 0.004627003 -0.5983324 1.2383432 0.10503633
## 78: 0.004794327 -0.4644118 1.0058356 0.11286204
## 79: 0.004794327 -0.4644118 1.0058356 0.11286204
##           se.bp          v         c       pchi

## [1] "NOIR_2" "ORF1"   "ORF55"  "ORF73"  "ORF62"
## [1] 5
## [1] "ORF28"   "ORF64_1" "ORF75"
## [1] 3

Selected number of clusters: 12

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  2:       1    ORF5 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  3:       1   ORF10 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  4:       1   ORF17 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  5:       1   ORF30 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  6:       1   ORF53 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  7:       1   ORF63 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  8:       1 ORF65_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
##  9:       1 ORF67_1 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 10:       1   ORF69 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 11:       1  NOIR_2 0.9834083 0.9970508 0.8173828 0.003528288 0.0007990959
## 12:       2    ORF2 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 13:       2    ORF3 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 14:       2   ORF11 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 15:       2   ORF14 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 16:       2   ORF18 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 17:       2   ORF19 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 18:       2   ORF26 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 19:       2   ORF29 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 20:       2   ORF37 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 21:       2   ORF51 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 22:       2   ORF55 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 23:       2 ORF66_1 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 24:       2   ORF73 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 25:       2   ORF76 0.8620495 0.9654496 0.6814089 0.017911175 0.0061014438
## 26:       3    ORF4 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 27:       3    ORF9 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 28:       3   ORF20 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 29:       3   ORF21 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 30:       3   ORF31 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 31:       3   ORF34 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 32:       3   ORF38 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 33:       3   ORF50 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 34:       3   ORF61 0.9804127 0.9971521 0.7428073 0.003866621 0.0007334090
## 35:       4    ORF6 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 36:       4   ORF70 0.9850740 0.9979508 0.7534348 0.003098568 0.0005522399
## 37:       5    ORF7 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 38:       5   ORF56 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 39:       5  NOIR_1 0.6756151 0.9634768 0.2633099 0.040259364 0.0072153033
## 40:       6    ORF8 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 41:       6   ORF22 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 42:       6   ORF23 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 43:       6   ORF24 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 44:       6   ORF25 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 45:       6   ORF33 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 46:       6 ORF35.5 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 47:       6   ORF36 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 48:       6   ORF39 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 49:       6     CTO 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 50:       6   ORF40 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 51:       6   ORF42 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 52:       6   ORF43 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 53:       6   ORF44 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 54:       6   ORF46 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 55:       6   ORF49 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 56:       6   ORF58 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 57:       6   ORF62 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 58:       6   ORF68 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 59:       6   ORF74 0.9067717 0.9829187 0.6224125 0.013399476 0.0033689002
## 60:       7   ORF12 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 61:       7   ORF13 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 62:       7   ORF15 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 63:       7   ORF16 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 64:       7   ORF35 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 65:       7   ORF41 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 66:       7   ORF48 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 67:       7   ORF52 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 68:       7   ORF54 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 69:       7   ORF57 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 70:       7   ORF60 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 71:       7   ORF71 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 72:       7   ORF72 0.9472084 0.9902116 0.7069614 0.008639267 0.0021296703
## 73:       8   ORF27 0.7904904 0.9662526 0.4397080 0.025548629 0.0060702951
## 74:       8   ORF59 0.7904904 0.9662526 0.4397080 0.025548629 0.0060702951
## 75:       9   ORF28 0.5315416 0.9101709 0.3441776 0.044014262 0.0134541621
## 76:      10   ORF32 0.9770332 0.9982955 0.5151696 0.004496626 0.0004626117
## 77:      11   ORF45 0.6926659 0.9668711 0.2610828 0.038775743 0.0066333119
## 78:      12 ORF64_1 0.5500885 0.9292526 0.2941077 0.045701573 0.0115867217
## 79:      12   ORF75 0.5500885 0.9292526 0.2941077 0.045701573 0.0115867217
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c       pchi
##           <num>      <num>     <num>      <num>
##  1: 0.004376930 -1.8294074 0.9239714 0.05335458
##  2: 0.004376930 -1.8294074 0.9239714 0.05335458
##  3: 0.004376930 -1.8294074 0.9239714 0.05335458
##  4: 0.004376930 -1.8294074 0.9239714 0.05335458
##  5: 0.004376930 -1.8294074 0.9239714 0.05335458
##  6: 0.004376930 -1.8294074 0.9239714 0.05335458
##  7: 0.004376930 -1.8294074 0.9239714 0.05335458
##  8: 0.004376930 -1.8294074 0.9239714 0.05335458
##  9: 0.004376930 -1.8294074 0.9239714 0.05335458
## 10: 0.004376930 -1.8294074 0.9239714 0.05335458
## 11: 0.004376930 -1.8294074 0.9239714 0.05335458
## 12: 0.005023951 -1.1447013 0.6730592 0.16333723
## 13: 0.005023951 -1.1447013 0.6730592 0.16333723
## 14: 0.005023951 -1.1447013 0.6730592 0.16333723
## 15: 0.005023951 -1.1447013 0.6730592 0.16333723
## 16: 0.005023951 -1.1447013 0.6730592 0.16333723
## 17: 0.005023951 -1.1447013 0.6730592 0.16333723
## 18: 0.005023951 -1.1447013 0.6730592 0.16333723
## 19: 0.005023951 -1.1447013 0.6730592 0.16333723
## 20: 0.005023951 -1.1447013 0.6730592 0.16333723
## 21: 0.005023951 -1.1447013 0.6730592 0.16333723
## 22: 0.005023951 -1.1447013 0.6730592 0.16333723
## 23: 0.005023951 -1.1447013 0.6730592 0.16333723
## 24: 0.005023951 -1.1447013 0.6730592 0.16333723
## 25: 0.005023951 -1.1447013 0.6730592 0.16333723
## 26: 0.004866876 -1.7084109 1.0563865 0.51628007
## 27: 0.004866876 -1.7084109 1.0563865 0.51628007
## 28: 0.004866876 -1.7084109 1.0563865 0.51628007
## 29: 0.004866876 -1.7084109 1.0563865 0.51628007
## 30: 0.004866876 -1.7084109 1.0563865 0.51628007
## 31: 0.004866876 -1.7084109 1.0563865 0.51628007
## 32: 0.004866876 -1.7084109 1.0563865 0.51628007
## 33: 0.004866876 -1.7084109 1.0563865 0.51628007
## 34: 0.004866876 -1.7084109 1.0563865 0.51628007
## 35: 0.004845179 -1.7779128 1.0925743 0.04880686
## 36: 0.004845179 -1.7779128 1.0925743 0.04880686
## 37: 0.004635436 -0.5796832 1.2128574 0.32603176
## 38: 0.004635436 -0.5796832 1.2128574 0.32603176
## 39: 0.004635436 -0.5796832 1.2128574 0.32603176
## 40: 0.005225222 -1.2149856 0.9031625 0.82402823
## 41: 0.005225222 -1.2149856 0.9031625 0.82402823
## 42: 0.005225222 -1.2149856 0.9031625 0.82402823
## 43: 0.005225222 -1.2149856 0.9031625 0.82402823
## 44: 0.005225222 -1.2149856 0.9031625 0.82402823
## 45: 0.005225222 -1.2149856 0.9031625 0.82402823
## 46: 0.005225222 -1.2149856 0.9031625 0.82402823
## 47: 0.005225222 -1.2149856 0.9031625 0.82402823
## 48: 0.005225222 -1.2149856 0.9031625 0.82402823
## 49: 0.005225222 -1.2149856 0.9031625 0.82402823
## 50: 0.005225222 -1.2149856 0.9031625 0.82402823
## 51: 0.005225222 -1.2149856 0.9031625 0.82402823
## 52: 0.005225222 -1.2149856 0.9031625 0.82402823
## 53: 0.005225222 -1.2149856 0.9031625 0.82402823
## 54: 0.005225222 -1.2149856 0.9031625 0.82402823
## 55: 0.005225222 -1.2149856 0.9031625 0.82402823
## 56: 0.005225222 -1.2149856 0.9031625 0.82402823
## 57: 0.005225222 -1.2149856 0.9031625 0.82402823
## 58: 0.005225222 -1.2149856 0.9031625 0.82402823
## 59: 0.005225222 -1.2149856 0.9031625 0.82402823
## 60: 0.004968046 -1.4394451 0.8949157 0.71371866
## 61: 0.004968046 -1.4394451 0.8949157 0.71371866
## 62: 0.004968046 -1.4394451 0.8949157 0.71371866
## 63: 0.004968046 -1.4394451 0.8949157 0.71371866
## 64: 0.004968046 -1.4394451 0.8949157 0.71371866
## 65: 0.004968046 -1.4394451 0.8949157 0.71371866
## 66: 0.004968046 -1.4394451 0.8949157 0.71371866
## 67: 0.004968046 -1.4394451 0.8949157 0.71371866
## 68: 0.004968046 -1.4394451 0.8949157 0.71371866
## 69: 0.004968046 -1.4394451 0.8949157 0.71371866
## 70: 0.004968046 -1.4394451 0.8949157 0.71371866
## 71: 0.004968046 -1.4394451 0.8949157 0.71371866
## 72: 0.004968046 -1.4394451 0.8949157 0.71371866
## 73: 0.005268284 -0.8383279 0.9900376 0.17121312
## 74: 0.005268284 -0.8383279 0.9900376 0.17121312
## 75: 0.005000790 -0.4703599 0.8714482 0.43210675
## 76: 0.005399375 -1.4831325 1.4450987 0.32741114
## 77: 0.004627003 -0.5983324 1.2383432 0.10503633
## 78: 0.004794327 -0.4644118 1.0058356 0.11286204
## 79: 0.004794327 -0.4644118 1.0058356 0.11286204
##           se.bp          v         c       pchi

## [1] "NOIR_2" "ORF1"   "ORF55"  "ORF73"  "ORF62"
## [1] 5
## [1] "ORF28"   "ORF64_1" "ORF75"
## [1] 3

Remove genes from clusters ?

## [1] "ORF28"   "ORF64_1" "ORF75"
## [1] 3
## No genes were removed from their corresponding clusters.
##     cluster     N
##       <int> <int>
##  1:       6    20
##  2:       2    14
##  3:       7    13
##  4:       1    11
##  5:       3     9
##  6:       5     3
##  7:       4     2
##  8:       8     2
##  9:      12     2
## 10:       9     1
## 11:      10     1
## 12:      11     1

Merge cluster stats

Assigning genes to clusters

Summarize and melt

Heatmaps

Normalized Expression

Expression delta ~ 6 hpi

Z-score of expression delta ~ 6 hpi

ORF kinetics, according to literature-based kinetic classes

Barplot of mean and SD

Figure 4 REVIEW - Mean and SD with linear connection

Mean and SD with loess function

Mean and SD with linear connection - Figure 4

Each replicate with loess

ORF kinetics, according to de-novo kinetic classes

Mean and SD with linear connection

Figure 5 REVIEW - Mean and SD with linear connection

Compare literature and de novo kinetic classes

NA shows the number of genes where the clustering did not yield an unambiguous result.

Combined Kinetic classes

De Novo Clusters

Literature clusters